Lake Erie has been affected by harmful algal blooms for decades. In 2014, this resulted in the plant having to shut down its intake after toxic cyanotoxins were found in source water. Such occurrences are becoming more common across the globe. U.S. EPA has established regulations for microcystin, the most common form of cyanotoxin. Climate change is predicted to increase the occurrence of other types of cyanotoxins, such as saxitoxins, which are not regulated by the U.S. EPA. Hence, the removal and monitoring of cyanotoxins, produced by harmful algae blooms, in water is of utmost importance to protect public health.The efficacy of oxidation varies greatly for each of the cyanotoxins due to their different chemical structures. There is presently no oxidation process that a water treatment plant can implement that is proven to simultaneously remove all the cyanotoxins (microcystin, saxitoxin, cylindrospermopsin, and anatoxin) from drinking water. Thus, water treatment plants that are currently designed to remove microcystins are not protected against all forms of cyanotoxins. The investigation of the removal of these cyanotoxins using innovative treatment technologies requires a detection method that is sensitive and capable of detecting all the variants of cyanotoxins. The detection of saxitoxin is particularly challenging as compared to other cyanotoxins due to its low molecular mass and highly polar nature. Hydrophilic interaction liquid chromatography coupled with mass spectrometry (HILIC-MS) has the ability to provide specific detection through mass differentiation, which makes it an ideal tool for the quantitative analysis of saxitoxin and its variants. Hence, a method was developed to extract and detect saxitoxin from water using HILIC-MS in conjunction with weak cation exchange solid phase extraction (SPE), to provide a sensitive and reliable quantification of saxitoxins. However, the application of LC/MS for the detection of cyanotoxins in treatment studies is not cost effective as the cost of instrumentation is high, its operation requires high skill, and cyanotoxin standards have limited access and are expensive. Hence, a screening technique has been developed which uses methylene blue to identify the reaction kinetics of persulfate and peroxide oxidation in the presence of ferrous chloride and to optimize parameters, which can be helpful in predicting the degradation of cyanotoxins under similar conditions. Catalyst activated persulfate and peroxide oxidation produce sulfate and hydroxyl radicals, which can degrade a wide range of recalcitrant chemicals and hence are preferred in water and wastewater treatment. The screening technique was validated by investigating the degradation of microcystin-LR. The notable advantages of developing this screening technique are: (i) reduced cost of analysis as methylene blue can be detected in real time by measuring its absorbance, and (ii) can perform multiple trials in short time due to ease of analysis. This screening technique was also applied to iron oxide coated ceramic membranes in combination with persulfate oxidation to understand the degradation kinetics.